title: Structural insights into cognate versus near-cognate discrimination during decoding.
abstract: The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.
authors.affiliation: Structural Biology Unit, CIC-bioGUNE, Derio, Basque Country, Spain.
authors.forename: Xabier
authors.initials: X
authors.lastname: Agirrezabala
authors.forename: Eduard
authors.initials: E
authors.lastname: Schreiner
authors.forename: Leonardo G
authors.initials: LG
authors.lastname: Trabuco
authors.forename: Jianlin
authors.initials: J
authors.lastname: Lei
authors.forename: Rodrigo F
authors.initials: RF
authors.lastname: Ortiz-Meoz
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.forename: Rachel
authors.initials: R
authors.lastname: Green
authors.forename: Joachim
authors.initials: J
authors.lastname: Frank
mesh_terms: D003062:Codon; D020285:Cryoelectron Microscopy; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D010444:Peptide Elongation Factor Tu / Q000737:chemistry* / Q000378:metabolism; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure
chemical_list: D003062:Codon; D012343:RNA, Transfer; D010444:Peptide Elongation Factor Tu